Multi Plot issues from ROI Manager

[S. Pagakis (IIBEAA)]

Hello everyone

We have RGB (3 colour fluorescence) images and we would like to plot a number of profiles along the SAME lines in each one of the R, G, B planes.

We use a composite image, ROI manager and the Multi PLot command

1) We have to do the Multi Plot command 3 times, once for each colour.  Which command can we use in a macro to switch the active plane of a composite image?
Stack.setActiveChannels("000");
doesn't seem to do what we want


2) The results file, the X coordinates column is repeated for each plot.   This is redundant info which makes the excel file twice as big.  Is there any way to suppress this, as it can be supressed in the PlotProfile (option K) command?

3) could the output for the 3 channels be output in the same "Plot Values" file?


Thank you in advance


******************************
Stamatis Pagakis Ph.D.
Head, Biological Imaging
Biomedical Research Foundation, Academy of Athens
Soranou Efessiou 4, Athens 115 27 - Greece
M:     [phone]                
W:     [phone]
FAX: [phone]
http://www.bioacademy.gr/faculty-details/HM4/Stamatis


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[Krs5]

Dear Stamatis,

You could try to use the macro Multi colour line profile plot  (see: https://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif/software-1/imagej-macros) or parts of its code which allows you to collect the data from all three planes in one go. It however will still repeat the x value for each channel even when in the same "Plot Values" file.

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif 

ImageJ workshops 15 and 16 December: http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif/workshops/imagej-workshops-15-and-16-December-2014 



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Stamatis Pagakis
Sent: 08 October 2014 16:28
To: [hidden email]
Subject: Multi Plot issues from ROI Manager

Hello everyone

We have RGB (3 colour fluorescence) images and we would like to plot a number of profiles along the SAME lines in each one of the R, G, B planes.

We use a composite image, ROI manager and the Multi PLot command

1) We have to do the Multi Plot command 3 times, once for each colour.  Which command can we use in a macro to switch the active plane of a composite image?
Stack.setActiveChannels("000");
doesn't seem to do what we want


2) The results file, the X coordinates column is repeated for each plot.   This is redundant info which makes the excel file twice as big.  Is there any way to suppress this, as it can be supressed in the PlotProfile (option K) command?

3) could the output for the 3 channels be output in the same "Plot Values" file?


Thank you in advance


******************************
Stamatis Pagakis Ph.D.
Head, Biological Imaging
Biomedical Research Foundation, Academy of Athens Soranou Efessiou 4, Athens 115 27 - Greece
M:     [phone]                
W:     [phone]
FAX: [phone]
http://www.bioacademy.gr/faculty-details/HM4/Stamatis


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[Rasband, Wayne (NIH/NIMH) [E]]

On Oct 8, 2014, at 11:28 AM, Stamatis Pagakis wrote:

> Hello everyone
>
> We have RGB (3 colour fluorescence) images and we would like to plot a number of profiles along the SAME lines in each one of the R, G, B planes.

The RGB Profile Plot macro at

    http://imagej.nih.gov/ij/macros/RGB_Profile_Plot.txt

does this.

> We use a composite image, ROI manager and the Multi PLot command
>
> 1) We have to do the Multi Plot command 3 times, once for each colour.  Which command can we use in a macro to switch the active plane of a composite image?
> Stack.setActiveChannels("000");
> doesn't seem to do what we want

Use the Stack.setChannel(c) macro function. For an example, refer to the RGB Profile Plot macro.
 
> 2) The results file, the X coordinates column is repeated for each plot.   This is redundant info which makes the excel file twice as big.  Is there any way to suppress this, as it can be supressed in the PlotProfile (option K) command?

Upgrade to the latest ImageJ daily build (1.49i14) and the duplicate x columns will not be repeated.

> 3) could the output for the 3 channels be output in the same "Plot Values" file?

The output of the RGB Profile Plot macro is saved to a single file.

-wayne
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[S. Pagakis (IIBEAA)]

Thank you Wayne for the quick response

I updated today to 1.49i15, but the Xn columns are still there.  

An obvious change from the previous version is that the format of the X columns has changed from integer to real with 3 decimal points.

Is there an option somewhere that I should switch off?

Thanks in advance


On 9 Oct, 2014, at 6:00 PM, "Rasband, Wayne (NIH/NIMH) [E]" <[hidden email]> wrote:

> On Oct 8, 2014, at 11:28 AM, Stamatis Pagakis wrote:
>
>> 2) The results file, the X coordinates column is repeated for each plot.   This is redundant info which makes the excel file twice as big.  Is there any way to suppress this, as it can be supressed in the PlotProfile (option K) command?
>
> Upgrade to the latest ImageJ daily build (1.49i14) and the duplicate x columns will not be repeated.
>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html


******************************
Stamatis Pagakis Ph.D.
Head, Biological Imaging
Biomedical Research Foundation, Academy of Athens
Soranou Efessiou 4, Athens 115 27 - Greece
M:     [phone]                
W:     [phone]
FAX: [phone]
http://www.bioacademy.gr/faculty-details/HM4/Stamatis


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